I've got to say, the Honda ad looks like CGI, especially the lighting and camera angles. The windscreen glass looked rendered too.
On the other one I see from the state of the singers that they must have had a few tries :-)

I too have a fascination with Rube Goldberg machines. Per your request, here are 2 I like:
http://www.flixxy.com/best-rube-goldberg-machine.htm
http://www.flixxy.com/rube-goldberg-fire-contraption.htm
Enjoy

The Cog ad is truly a masterpiece. Years ago I remember a video interview with the director in which he talked about what an exhausting effort it was to shoot this and how many dozens of 'takes' were required to get everything working perfectly. There are no edits or movie tricks involved -- it is all real, exactly as it looks.
On another note, I wonder how many engineers have had the experience of debugging a design that was worthy of being called a Rube Goldberg?
I have seen way too many such designs in my career -- if there is a simple way to do something, and a much more complicated way to do it, some designers will for some reason take the most convoluted, complex, tortuous path to get from A to B, creating an un-debuggable, un-reusable nightmare of a design in the process. You guys know who you are!
Every design should begin with a medidation using the KISS principle as the mantra: Keep It Simple Stupid, Keep It Simple Stupid...(repeat as necessary).